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At least 1,153 records · Page 64

Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)

Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.

60 APPLIED LIFE SCIENCES↗

Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted post hoc tests for genotype-by-environment interaction, using a mixed model ANOVA. We found that 8 of the 54 SNPs showed significant GxE. Candidate genes underlying variation in root pulling force included those involved in nutrient transport. Although they are often treated separately, variation in the ability of plant roots to sense and respond to variation in environmental resources including water and nutrients may be linked by the genes and pathways underlying this variation. While functional validation of the identified genes is needed, our results expand the current knowledge of root phenotypic plasticity at the whole plant and gene levels, and further elucidate the complex genetic architecture of maize root systems.

Woods, Patrick↗

Statistical Homogenization of Elastic and Fracture Properties of a Sample Selective Laser Melting Material

Selective laser melting (SLM) is an additive manufacturing technique commonly used in the rapid prototyping of components. The complexity of the SLM microstructure poses a unique challenge to deriving effective mechanical properties at different length scales. Representative volume elements (RVEs) are often used to homogenize the material properties of composites. Instead of RVEs, we use statistical volume elements (SVEs) to homogenize the elastic and fracture properties of the material. This relates the inherent variation of a material’s microstructure to the variation in its mechanical properties at different observation scales. The convergence to the RVE limit is examined from two perspectives: the stability of the mean value as the SVE size increases for the mean-based approach, and the tendency of the normalized variation in homogenized properties to zero as the SVE size increases for the variation-based approach. Fracture properties tend to make the RVE limit slower than do elastic properties from both perspectives. There are also differences between vertical (normal to printing plane) and horizontal (in-plane) properties. While the elastic properties tend to make the RVE limit faster for the horizontal direction, i.e., having a smaller variation and more stable mean value, the fracture properties exhibit the opposite effect. We attributed these differences to the geometry of the melt pools.

36 MATERIALS SCIENCE↗

Do Genetic Drift and Gene Flow Affect the Geographic Distribution of Female Plants in Gynodioecious Lobelia siphilitica?

Variation in population sex ratio is particularly pronounced in gynodioecious angiosperms. Extremely high female frequencies in gynodioecious populations cannot be readily explained by selective forces alone. To assess the contributions of drift and gene flow to extreme sex-ratio variation, we documented sex ratio and population size in 92 populations of Lobelia siphilitica across its range and genotyped plants using plastid and nuclear genetic markers. Similarity in spatial patterns of genetic and demographic variables may suggest that drift and/or gene flow have contributed to population sex-ratio variation in L. siphilitica. We found strong spatial structuring of extremely high female frequencies: populations with >50% female plants are restricted to the south–central portion of the range. However, we did not detect any spatial structuring in population size nor metrics of genetic diversity, suggesting that extreme variation in female frequency is not strongly affected by drift or gene flow. Extreme sex-ratio variation is frequently observed in gynodioecious plants, but its causes are difficult to identify. Further investigation into mechanisms that create or maintain the spatial structure of sex ratios in gynodioecious species will provide much needed insight.

54 ENVIRONMENTAL SCIENCES↗

GPS Measurements of Precipitable Water Vapor Can Improve Survey Calibration: A Demonstration from KPNO and the Mayall z -band Legacy Survey

Dual-band Global Positioning Satellite (GPS) measurements of precipitable water vapor (PWV) at the Kitt Peak National Observatory predict the overall per-image sensitivity of the Mayall z-band Legacy Survey (MzLS). The per-image variation in the brightness of individual stars is strongly correlated with the measured PWV and the color of the star. Synthetic stellar spectra through TAPAS transmission models successfully predict the observed PWV-induced photometric variation. We find that PWV absorption can be well approximated by a linear relationship with (airmass × PWV) 0.6 and present an update on the traditional treatment in the literature. The MzLS zero-point sensitivity in electrons s –1 varies with a normalized-mean absolute deviation of 61 mmag. PWV variation accounts 23 mmag of this zero-point variation. The MzLS per-image absolute sensitivity decreases by 40 mmag per effective mm of PWV. The overall gray offset portion of this variation is corrected by the calibration to a reference catalog. But the relative calibration error between blue (r – z < 0.5 mag) versus red (1.2 mag < r – z) stars increases by 0.3–2 mmag per effective mm of PWV. We argue that GPS systems provide more precise PWV measurements than using differential measurements of stars of different colors and recommend that observatories install dual-band GPS as a low-maintenance, low-cost, auxiliary calibration system. We extend our results of the need for well-calibrated PWV measurements by presenting the calculations of the PWV photometric impact on three science cases of interest: stellar photometry, supernova cosmology, and quasar identification and variability.

79 ASTRONOMY AND ASTROPHYSICS↗

The DREAMS Project: Disentangling the Impact of Halo-to-halo Variance and Baryonic Feedback on Milky Way Dark Matter Density Profiles

In this work, we utilize a new suite of Milky Way–mass halos from the DREAMS Project, simulated with cold dark matter (CDM), to quantify the influence of baryon feedback and intrinsic halo-to-halo variance on dark matter density profiles. Our suite of 1024 halos varies over supernova and black hole feedback parameters from the IllustrisTNG model, as well as variations in two cosmological parameters. We find that, for the DREAMS parameter variations, Milky Way–mass dark matter density profiles in the IllustrisTNG model are largely insensitive to astrophysics and cosmology variations, with the dominant source of scatter instead arising from halo-to-halo variance. However, most of the (comparatively minor) feedback-driven variations come from the changes to supernova prescriptions. By comparing to dark-matter-only simulations, we find that the strongest supernova wind energies are so effective at preventing galaxy formation that the halos are nearly entirely collisionless dark matter. Finally, regardless of physics variation, all of the DREAMS halos are roughly consistent with a halo contracting adiabatically from the presence of baryons, unlike models that have bursty stellar feedback. This work represents a step toward assessing the uncertainty in Milky Way dark matter profiles, with direct implications for dark matter searches where systematic uncertainty in the density profile remains a major challenge.

Garcia, Alex M. [University of Virginia, Charlotte↗

Unraveling the Complex Behavior of Mrk 421 with Simultaneous X-Ray and VHE Observations during an Extreme Flaring Activity in 2013 April

Here we report on a multiband variability and correlation study of the TeV blazar Mrk 421 during an exceptional flaring activity observed from 2013 April 11 to 19. The study uses, among others, data from GLAST-AGILE Support Program (GASP) of the Whole Earth Blazar Telescope (WEBT), Swift, Nuclear Spectroscopic Telescope Array (NuSTAR), Fermi Large Area Telescope, Very Energetic Radiation Imaging Telescope Array System (VERITAS), and Major Atmospheric Gamma Imaging Cherenkov (MAGIC). The large blazar activity and the 43 hr of simultaneous NuSTAR and MAGIC/VERITAS observations permitted variability studies on 15 minute time bins over three X-ray bands (3–7 keV, 7–30 keV, and 30–80 keV) and three very-high-energy (VHE; >0.1 TeV) gamma-ray bands (0.2–0.4 TeV, 0.4–0.8 TeV, and >0.8 TeV). We detected substantial flux variations on multi-hour and sub-hour timescales in all of the X-ray and VHE gamma-ray bands. The characteristics of the sub-hour flux variations are essentially energy independent, while the multi-hour flux variations can have a strong dependence on the energy of the X-rays and the VHE gamma-rays. The three VHE bands and the three X-ray bands are positively correlated with no time lag, but the strength and characteristics of the correlation change substantially over time and across energy bands. Our findings favor multi-zone scenarios for explaining the achromatic/chromatic variability of the fast/slow components of the light curves, as well as the changes in the flux–flux correlation on day-long timescales. We interpret these results within a magnetic reconnection scenario, where the multi-hour flux variations are dominated by the combined emission from various plasmoids of different sizes and velocities, while the sub-hour flux variations are dominated by the emission from a single small plasmoid moving across the magnetic reconnection layer.

79 ASTRONOMY AND ASTROPHYSICS↗

Microstructural Characterization of A709 Commercial Heats with Precipitation Treatment

This report discusses work conducted at Idaho National Laboratory in fiscal year 2022 associated with the precipitates in Alloy 709 (A709). The purpose of this work is to support the development of the A709 Code Cases to qualify A709 in Section III, Division 5 of the American Society of Mechanical Engineers Boiler and Pressure Vessel Code. This would permit the use of A709 for elevated-temperature nuclear construction. This work encompassed two broad goals. The first goal was to understand the microstructure of the second commercial heat of plate A709 purchased through the Advanced Reactors Technologies Program in both the solution-annealed and precipitation-treated conditions. Transmission electron microscopy was utilized to characterize these microstructures. Direct comparisons were then made between the solution-annealed and precipitation-treated conditions as well as between the first and second commercial heats of plate A709. The second goal was to understand the impact of variations in the time and temperature of the precipitation treatment on the properties of A709. The precipitation treatment temperature was varied from 750°C to 800°C for times ranging from 3 hours to 30 hours. The hardness of each precipitation treatment variation was measured. All of the precipitation treatment variations investigated besides a specimen from the second commercial heat of plate A709 precipitation treated at 800? for 9 hours met the room-temperature hardness requirement specified in ASTM A213 and SA-213 for UNS S31025. The hardness measured for the specimen from the second commercial heat of plate A709 that was precipitation treated at 800? for 9 hours is considered an outlier. The next step is to look at the extremes of the precipitation treatment variations investigated and conduct elevated-temperature mechanical testing. The purpose of this testing would be to assess if these time and temperature variations have any impact on the mechanical performance.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Uncertainty quantification of graph convolution neural network models of evolving processes

The application of neural network models to scientific machine learning tasks has proliferated in recent years. In particular, neural networks have proved to be adept at modeling processes with spatial–temporal complexity. Nevertheless, these highly parameterized models have garnered skepticism in their ability to produce outputs with quantified error bounds over the regimes of interest. Hence there is a need to find uncertainty quantification methods that are suitable for neural networks. In this work we present comparisons of the parametric uncertainty quantification of neural networks modeling complex spatial–temporal processes with Hamiltonian Monte Carlo and Stein variational gradient descent and its projected variant. Specifically we apply these methods to graph convolutional neural network models of evolving systems modeled with recurrent neural network and neural ordinary differential equations architectures. We show that Stein variational inference is a viable alternative to Monte Carlo methods with some clear advantages for complex neural network models. For our exemplars, Stein variational interference gave similar pushed forward uncertainty profiles through time compared to Hamiltonian Monte Carlo, albeit with generally more generous variance. As a result, projected Stein variational gradient descent also produced similar uncertainty profiles to the non-projected counterpart, but large reductions in the active weight space were confounded by the stability of the neural network predictions and the convoluted likelihood landscape.

36 MATERIALS SCIENCE↗

Possible Superconductivity with a Bogoliubov Fermi Surface in a Lightly Doped Kagome U(1) Spin Liquid

Whether the doped t-J model on the Kagome lattice supports exotic superconductivity has not been decisively answered. In this paper, we propose a new class of variational states for this model and perform large-scale variational Monte Carlo simulation on it. The proposed variational states are parameterized by the SU(2)-gauge-rotation angles, as the SU(2)-gauge structure hidden in the Gutzwiller-projected mean-field ansatz for the undoped model is broken upon doping. These variational doped states smoothly connect to the previously studied U(1) π-flux or 0-flux states, and energy minimization among them yields a chiral noncentrosymmetric nematic superconducting state with 2 × 2-enlarged unit cell. Moreover, this pair density wave state possesses a finite Fermi surface for the Bogoliubov quasi particles. We further study experimentally relevant properties of this intriguing pairing state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence–absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.

Thlaspi arvense↗

Posterior Covariance Matrix Approximations

Here, the Davis equation of state (EOS) is commonly used to model thermodynamic relationships for high explosive (HE) reactants. Typically, the parameters in the EOS are calibrated, with uncertainty, using a Bayesian framework and Markov Chain Monte Carlo (MCMC) methods. However, MCMC methods are computationally expensive, especially for complex models with many parameters. This paper provides a comparison between MCMC and less computationally expensive Variational methods (Variational Bayesian and Hessian Variational Bayesian) for computing the posterior distribution and approximating the posterior covariance matrix based on heterogeneous experimental data. All three methods recover similar posterior distributions and posterior covariance matrices. This study demonstrates that for this EOS parameter calibration application, the assumptions made in the two Variational methods significantly reduce the computational cost but do not substantially change the results compared to MCMC.

97 MATHEMATICS AND COMPUTING↗

Oxidation and pyrolysis of methyl propyl ether

The ignition, oxidation, and pyrolysis chemistry of methyl propyl ether (MPE) was probed experimentally at several different conditions, and a comprehensive chemical kinetic model was constructed to help understand the observations, with many of the key parameters computed using quantum chemistry and transition state theory. Experiments were carried out in a shock tube measuring time variation of CO concentrations, in a flow tube measuring product concentrations, and in a rapid compression machine (RCM) measuring ignition delay times. The detailed reaction mechanism was constructed using the Reaction Mechanism Generator software. Sensitivity and flux analyses were used to identify key rate and thermochemical parameters, which were then computed using quantum chemistry to improve the mechanism. Validation of the final model against the 1-20 bar 600-1500 K experimental data is presented with a discussion of the kinetics. The model is in excellent agreement with most of the shock tube and RCM data. Strong non-monotonic variation in conversion and product distribution is observed in the flow-tube experiments as the temperature is increased, and unusually strong pressure dependence and significant heat release during the compression stroke is observed in the RCM experiments. These observations are largely explained by a close competition between radical decomposition and addition to O2 at different sites in MPE; this causes small shifts in conditions to lead to big shifts in the dominant reaction pathways. The validated mechanism was used to study the chemistry occurring during ignition in a diesel engine, simulated using Ignition Quality Test (IQT) conditions. At the IQT conditions, where the MPE concentration is higher, bimolecular reactions of peroxy radicals are much more important than in the RCM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CO 2 storage site characterization using ensemble-based approaches with deep generative models

Estimating spatially distributed properties such as permeability from available sparse measurements is a great challenge in efficient subsurface CO 2 storage operations. In this paper, a deep generative model that can accurately capture complex subsurface structure is tested with an ensemble-based inversion method for accurate and accelerated characterization of CO 2 storage sites. We chose Wasserstein Generative Adversarial Network with Gradient Penalty (WGAN-GP) for its realistic reservoir property representation and Ensemble Smoother with Multiple Data Assimilation (ES-MDA) for its robust data fitting and uncertainty quantification capability. WGAN-GP are trained to generate high-dimensional permeability fields from a low-dimensional latent space and ES-MDA then updates the latent variables by assimilating available measurements. Several subsurface site characterization examples including Gaussian, channelized, and fractured reservoirs are used to evaluate the accuracy and computational efficiency of the proposed method and the main features of the unknown permeability fields are characterized accurately with reliable uncertainty quantification. Furthermore, the estimation performance is compared with a widely-used variational, i.e., optimization-based, inversion approach, and the proposed approach outperforms the variational inversion method in several benchmark cases. We explain such superior performance by visualizing the objective function in the latent space: because of nonlinear and aggressive dimension reduction via generative modeling, the objective function surface becomes extremely complex while the ensemble approximation can smooth out the multi-modal surface during the minimization. This suggests that the ensemble-based approach works well over the variational approach when combined with deep generative models at the cost of forward model runs unless convergence-ensuring modifications are implemented in the variational inversion.

42 ENGINEERING↗

A careful examination of closure models in Euler–Lagrange Simulations of compressible multiphase flow in a planar shock particle curtain problem

In this work we present a comprehensive investigation of state-of-the-art closure models employed to represent interphase momentum, thermal, and work exchange between the gas and particulate phases for Euler–Lagrange (EL) simulations in shock-driven flows. A complete list of closures for the force, torque, heat transfer, and work exchange models is provided. In particular, the present work includes a stochastic closure for the particle-to-particle variation in the quasi-steady force and a deterministic closure for particle-to-particle variation in the added mass force in an EL framework. These variations arise due to the presence of neighboring particles and particle–particle interactions. To investigate the importance of each closure term, we carry out fully three-dimensional simulations for a planar shock propagating over a random bed of inert particles. The primary goal is to evaluate the role of each closure term on the gas dynamic features (such as transmitted and reflected shock locations) and particle curtain features (such as upstream and downstream curtain locations). To this end, thirteen cases are considered, with each case progressively including a closure model with the goal to identify and quantify its contribution to the simulated dynamics. We show that the volume fraction dependence of the mean force models plays an important role in generating wave-like instabilities that lead to concentration bands. In addition, fluctuations in quasi-steady and added mass forces primarily decrease the internal instabilities that tend to enhance local volume fraction variations. Particle rotation is primarily due to inter-particle collisions, is generally weak, and does not play an important role in the translational dynamics for the present configuration. Inter-phase heat transfer has a strong effect on gas phase temperature, slows down the transmitted and reflected shocks, and decreases the width of the curtain. Furthermore, the absence of a work-coupling model fails to conserve the total energy, greatly under-predicts the gas temperature which in turn affects the particle dynamics.

Compressible flow↗

Accelerated thermal property mapping of TRISO advanced nuclear fuel

TRistructural ISOtropic (TRISO) fuel is a leading-edge nuclear fuel form representing a departure from the more traditional nuclear fuel forms utilized in the reactor fleet of today. Rather than a monolithic fuel pellet of uranium dioxide, integral fuel forms containing TRISO fuel are composed of thousands of microencapsulated uranium-bearing fuel kernels and individually coated with multiple layers of pyrolytic carbon and silicon carbide. These multilayered ceramic coatings serve as an environmental barrier to ensure radioactive and chemically reactive fission products are contained within the reactor fuel elements, but also participate in the transfer of heat generated in the nuclear fuel to the coolant – the primary purpose of a nuclear reactor. Since traditional thermal property measurement techniques, such as laser flash analysis, would be unable to resolve the thermal properties of the individual TRISO coating layers, a simplified frequency-domain thermoreflectance technique has been developed to rapidly map the thermal properties of TRISO particles. Using this technique, the thermal properties of TRISO particles have been mapped from room temperature up to 1000 °C to examine the spatial variation and temperature-dependency of the thermal properties within each layer. Additionally, spatial-domain thermoreflectance was used to examine the anisotropy of the thermal properties for each layer at different locations within a single TRISO particle, and across multiple TRISO particles to assess the intra- and inter-particle uniformity of thermal properties, respectively. To elucidate the underlying causes for the measured variations in thermal properties, scanning electron microscopy and Raman spectroscopy were used to examine variations in microstructure and chemical bonding within the different coating layers. Results from this work are then compared with previous examinations of TRISO fuel particles and microstructurally driven mechanisms for the variations in the measured thermal properties of the different carbonaceous layers are discussed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Impact of ferromagnetic electrode length and thickness on Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSD)

A knowledge gap exists about the impact of variation in length and thickness of ferromagnetic(FM) electrodes on molecular spintronics devices’ ability to manifest molecular coupling impact. Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSDs) are potential candidates for inventing highly correlated materials and devices and investigating the fundamental science of organic spintronics. This paper reports our experi- mental observations providing the dramatic impact of variation in ferromagnetic electrode length and thickness on paramagnetic molecule-based MTJMSD. Room temperature transport studies were performed to investigate the effect of FM electrode thickness. On the other hand, magnetic force microscopy measurements were con- ducted to understand the effect of FM electrode length extending beyond the molecular junction area, i.e., the site where paramagnetic molecules bridged between two FM. In the strong molecular coupling regime, transport study suggested thickness variation caused ~1000 to million-fold differences in junction conductivity. MFM study revealed near-zero magnetic contrast for pillar-shaped MTJMSD without any extended FM electrode. However, MFM images showed a multitude of microscopic magnetic phases on cross junction shaped MTJMSD where FM electrodes extended beyond the junction area. To understand the intriguing experimental results, we conducted an in-depth theoretical study using Monte Carlo Simulation (MCS) approach. MCS study utilized a Heisenberg atomic model of cross junction shaped MTJMSD to gain insights about room temperature transport and MFM experimental observations of microscopic MTJMSD. To make this study applicable for a wide variety of MTJMSDs, we systematically studied the effect of variation in molecular coupling strength between magnetic molecules and ferromagnetic (FM) electrodes of various dimensions. Here, our theoretical results suggest 25 atoms thick FM electrode show very weak molecular coupling impact and of the same order of experimentally studied FM electrode dimensions showing weak effect. Also, MCS results agree with experimentally observed multiple magnetic phases on lengthy FM electrodes of an MTJMSD.

42 ENGINEERING↗